tbuckley/cabot-search huggingface dataset:
BH3 mimetics and azacitidine show synergistic effects on juvenile myelomonocytic leukemia
Authors: Ying Wu, Patricia M. A. Zehnle, Jovana Rajak, Naile Koleci, Geoffroy Andrieux, Lorena Gallego-Villar, Konrad Aumann, Melanie Boerries, Charlotte M. Niemeyer, Christian Flotho, Sheila Bohler, Miriam Erlacher
Journal: Leukemia (2023)

Abstract Juvenile myelomonocytic leukemia (JMML) is an aggressive hematopoietic disorder of infancy and early childhood driven by constitutively active RAS signaling and characterized by abnormal proliferation of the granulocytic-monocytic blood cell lineage. Most JMML patients require hematopoietic stem cell transplantation for cure, but the risk of relapse is high for some JMML subtypes. Azacitidine was shown to effectively reduce leukemic burden in a subset of JMML patients. However, variable response rates to azacitidine and the risk of drug resistance highlight the need for novel therapeutic approaches. Since RAS signaling is known to interfere with the intrinsic apoptosis pathway, we combined various BH3 mimetic drugs with azacitidine in our previously established patient-derived xenograft model. We demonstrate that JMML cells require both MCL-1 and BCL-X L for survival, and that these proteins can be effectively targeted by azacitidine and BH3 mimetic combination treatment. In vivo azacitidine acts via downregulation of antiapoptotic MCL-1 and upregulation of proapoptotic BH3-only. The combination of azacitidine with BCL-X L inhibition was superior to BCL-2 inhibition in eliminating JMML cells. Our findings emphasize the need to develop clinically applicable MCL-1 or BCL-X L inhibitors in order to enable novel combination therapies in JMML refractory to standard therapy.
Synthetic chromosome fusion: Effects on mitotic and meiotic genome structure and function
Authors: Jingchuan Luo, Luis A. Vale-Silva, Adhithi R. Raghavan, Guillaume Mercy, Jonna Heldrich, Xiaoji Sun, Mingyu Kenneth Li, Weimin Zhang, Neta Agmon, Kun Yang, Jitong Cai, Giovanni Stracquadanio, Agnès Thierry, Yu Zhao, Camila Coelho, Laura H. McCulloch, Stephanie Lauer, David B. Kaback, Joel S. Bader, Leslie A. Mitchell, Julien Mozziconacci, Romain Koszul, Andreas Hochwagen, Jef D. Boeke, Greg Adoff, Ju Young Ahn, Anvesh Annadanam, Surekha Annadanam, Henri Berger, Yi Chen, Michael Chickering, Andrew D’Avino, Oren Fishman, Jay Im, Sangmin Kim, Sunghan Kim, Hong Seo Lim, Lauren Meyer, Allison Moyer, Natalie A. Murphy, Peter Natov, Arthur Radley, Lisa Scheifele, Arushi Tripathy, Rebeca Vergara Greeno, Tony Wang, Nick Wilkerson, Karen Zeller, Tony Zheng, Vivian Zhou
Journal: Cell Genomics (2023)

We designed and synthesized synI, which is ∼21.6% shorter than native chrI, the smallest chromosome in Saccharomyces cerevisiae. SynI was designed for attachment to another synthetic chromosome due to concerns surrounding potential instability and karyotype imbalance and is now attached to synIII, yielding the first synthetic yeast fusion chromosome. Additional fusion chromosomes were constructed to study nuclear function. ChrIII-I and chrIX-III-I fusion chromosomes have twisted structures, which depend on silencing protein Sir3. As a smaller chromosome, chrI also faces special challenges in assuring meiotic crossovers required for efficient homolog disjunction. Centromere deletions into fusion chromosomes revealed opposing effects of core centromeres and pericentromeres in modulating deposition of the crossover-promoting protein Red1. These effects extend over 100 kb and promote disproportionate Red1 enrichment, and thus crossover potential, on small chromosomes like chrI. These findings reveal the power of synthetic genomics to uncover new biology and deconvolute complex biological systems.
A spotlight on global collaboration in the Sc2.0 yeast consortium
Authors: Junbiao Dai, Huanming Yang, Isak S. Pretorius, Yizhi Cai, Chantal Yue Shen, Matthew Chang, Yingjin Yuan
Journal: Cell Genomics (2023)

The Synthetic Yeast Genome Project (Sc2.0) is an international collaboration that aims to create and optimize synthetic versions of each Saccharomyces cerevisiae chromosome, with the ultimate goal of assembling a yeast organism with a synthetic with design features facilitating applications in synthetic biology and engineering projects. The consortium research groups are global, and, here, we highlight the work of the China-based Sc2.0 researchers and their thoughts on the future of Sc2.0 and synthetic biology.
Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast
Authors: Yue Shen, Feng Gao, Yun Wang, Yuerong Wang, Ju Zheng, Jianhui Gong, Jintao Zhang, Zhouqing Luo, Daniel Schindler, Yang Deng, Weichao Ding, Tao Lin, Reem Swidah, Hongcui Zhao, Shuangying Jiang, Cheng Zeng, Shihong Chen, Tai Chen, Yong Wang, Yisha Luo, Leslie Mitchell, Joel S Bader, Guojie Zhang, Xia Shen, Jian Wang, Xian Fu, Junbiao Dai, Jef D Boeke, Huanming Yang, Xun Xu, Yizhi Cai
Journal: Cell Genomics (2023)

Aneuploidy compromises genomic stability, often leading to embryo inviability, and is frequently associated with tumorigenesis and aging. Different aneuploid chromosome stoichiometries lead to distinct transcriptomic and phenotypic changes, making it helpful to study aneuploidy in tightly controlled genetic backgrounds. By deploying the engineered SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) system to the newly synthesized megabase Sc2.0 chromosome VII (synVII), we constructed a synthetic disomic yeast and screened hundreds of SCRaMbLEd derivatives with diverse chromosomal rearrangements. Phenotypic characterization and multi-omics analysis revealed that fitness defects associated with aneuploidy could be restored by (1) removing most of the chromosome content or (2) modifying specific regions in the duplicated chromosome. These findings indicate that both chromosome copy number and specific chromosomal regions contribute to the aneuploidy-related phenotypes, and the synthetic chromosome resource opens new paradigms in studying aneuploidy.
Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects
Authors: Thomas C. Williams, Heinrich Kroukamp, Xin Xu, Elizabeth L.I. Wightman, Briardo Llorente, Anthony R. Borneman, Alexander C. Carpenter, Niel Van Wyk, Felix Meier, Thomas R.V. Collier, Monica I. Espinosa, Elizabeth L. Daniel, Roy S.K. Walker, Yizhi Cai, Helena K.M. Nevalainen, Natalie C. Curach, Ira W. Deveson, Timothy R. Mercer, Daniel L. Johnson, Leslie A. Mitchell, Joel S. Bader, Giovanni Stracquadanio, Jef D. Boeke, Hugh D. Goold, Isak S. Pretorius, Ian T. Paulsen
Journal: Cell Genomics (2023)

Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.
Genome-wide meta-analysis, functional genomics and integrative analyses implicate new risk genes and therapeutic targets for anxiety disorders
Authors: Wenqiang Li, Rui Chen, Laipeng Feng, Xinglun Dang, Jiewei Liu, Tengfei Chen, Jinfeng Yang, Xi Su, Luxian Lv, Tao Li, Zhijun Zhang, Xiong-Jian Luo
Journal: Nature Human Behaviour (2023)
Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains
Authors: Laura H. McCulloch, Vijayan Sambasivam, Amanda L. Hughes, Narayana Annaluru, Sivaprakash Ramalingam, Viola Fanfani, Evgenii Lobzaev, Leslie A. Mitchell, Jitong Cai, Hua Jiang, John LaCava, Martin S. Taylor, William R. Bishai, Giovanni Stracquadanio, Lars M. Steinmetz, Joel S. Bader, Weimin Zhang, Jef D. Boeke, Srinivasan Chandrasegaran, Breeana G. Anderson, Abena Apaw, Pavlo Bohutskyi, Erin Buchanan, Daniel Chang, Melinda Chen, Eric Cooper, Amanda Deliere, Kallie Drakos, Justin Dubin, Christopher Fernandez, Zheyuan Guo, Thomas Harrelson, Dongwon Lee, Jessica McDade, Scott Melamed, Héloise Müller, Adithya Murali, José U. Niño Rivera, Mira Patel, Mary Rodley, Jenna Schwarz, Nirav Shelat, Josh S. Sims, Barrett Steinberg, James Steinhardt, Rishi K. Trivedi, Christopher Von Dollen, Tianyi Wang, Remus Wong, Yijie Xu, Noah Young, Karen Zeller, Allen Zhang
Journal: Cell Genomics (2023)

We describe the complete synthesis, assembly, debugging, and characterization of a synthetic 404,963 bp chromosome,
Optogenetic stimulation of vagal nerves for enhanced glucose-stimulated insulin secretion and β cell proliferation
Authors: Yohei Kawana, Junta Imai, Yosuke M. Morizawa, Yoko Ikoma, Masato Kohata, Hiroshi Komamura, Toshihiro Sato, Tomohito Izumi, Junpei Yamamoto, Akira Endo, Hiroto Sugawara, Haremaru Kubo, Shinichiro Hosaka, Yuichiro Munakata, Yoichiro Asai, Shinjiro Kodama, Kei Takahashi, Keizo Kaneko, Shojiro Sawada, Tetsuya Yamada, Akira Ito, Kuniyasu Niizuma, Teiji Tominaga, Akihiro Yamanaka, Ko Matsui, Hideki Katagiri
Journal: Nature Biomedical Engineering (2023)

The enhancement of insulin secretion and of the proliferation of pancreatic β cells are promising therapeutic options for diabetes. Signals from the vagal nerve regulate both processes, yet the effectiveness of stimulating the nerve is unclear, owing to a lack of techniques for doing it so selectively and prolongedly. Here we report two optogenetic methods for vagal-nerve stimulation that led to enhanced glucose-stimulated insulin secretion and to β cell proliferation in mice expressing choline acetyltransferase-channelrhodopsin 2. One method involves subdiaphragmatic implantation of an optical fibre for the photostimulation of cholinergic neurons expressing a blue-light-sensitive opsin. The other method, which suppressed streptozotocin-induced hyperglycaemia in the mice, involves the selective activation of vagal fibres by placing blue-light-emitting lanthanide microparticles in the pancreatic ducts of opsin-expressing mice, followed by near-infrared illumination. The two methods show that signals from the vagal nerve, especially from nerve fibres innervating the pancreas, are sufficient to regulate insulin secretion and β cell proliferation.
High replicability of newly discovered social-behavioural findings is achievable
Authors: John Protzko, Jon Krosnick, Leif Nelson, Brian A Nosek, Jordan Axt, Matt Berent, Nicholas Buttrick, Matthew DeBell, Charles R Ebersole, Sebastian Lundmark, Bo MacInnis, Michael O'Donnell, Hannah Perfecto, James E Pustejovsky, Scott S Roeder, Jan Walleczek, Jonathan W Schooler
Journal: Nature Human Behaviour (2023)

Failures to replicate evidence of new discoveries have forced scientists to ask whether this unreliability is due to suboptimal implementation of methods or whether presumptively optimal methods are not, in fact, optimal. This paper reports an investigation by four coordinated laboratories of the prospective replicability of 16 novel experimental findings using rigour-enhancing practices: confirmatory tests, large sample sizes, preregistration and methodological transparency. In contrast to past systematic replication efforts that reported replication rates averaging 50%, replication attempts here produced the expected effects with significance testing (P < 0.05) in 86% of attempts, slightly exceeding the maximum expected replicability based on observed effect sizes and sample sizes. When one lab attempted to replicate an effect discovered by another lab, the effect size in the replications was 97% that in the original study. This high replication rate justifies confidence in rigour-enhancing methods to increase the replicability of new discoveries.
Establishing chromosomal design-build-test-learn through a synthetic chromosome and its combinatorial reconfiguration
Authors: Jee Loon Foo, Shohei Kitano, Adelia Vicanatalita Susanto, Zhu Jin, Yicong Lin, Zhouqing Luo, Linsen Huang, Zhenzhen Liang, Leslie A. Mitchell, Kun Yang, Adison Wong, Yizhi Cai, Jitong Cai, Giovanni Stracquadanio, Joel S. Bader, Jef D. Boeke, Junbiao Dai, Matthew Wook Chang
Journal: Cell Genomics (2023)

Chromosome-level design-build-test-learn cycles (chrDBTLs) allow systematic combinatorial reconfiguration of chromosomes with ease. Here, we established chrDBTL with a redesigned synthetic Saccharomyces cerevisiae chromosome XV, synXV. We designed and built synXV to harbor strategically inserted features, modified elements, and synonymously recoded genes throughout the chromosome. Based on the recoded chromosome, we developed a method to enable chrDBTL: CRISPR-Cas9-mediated mitotic recombination with endoreduplication (CRIMiRE). CRIMiRE allowed the creation of customized wild-type/synthetic combinations, accelerating genotype-phenotype mapping and synthetic chromosome redesign. We also leveraged synXV as a "build-to-learn" model organism for translation studies by ribosome profiling. We conducted a locus-to-locus comparison of ribosome occupancy between synXV and the wild-type chromosome, providing insight into the effects of codon changes and redesigned features on translation dynamics in vivo. Overall, we established synXV as a versatile reconfigurable system that advances chrDBTL for understanding biological mechanisms and engineering strains.
PDGFRβ Signaling Cooperates with β-Catenin to Modulate c-Abl and Biologic Behavior of Desmoid-Type Fibromatosis
Authors: Jia Hu, Meera R. Hameed, Narasimhan P. Agaram, Karissa A. Whiting, Li-Xuan Qin, Anthony M. Villano, Rachael B. O'Connor, Julian M. Rozenberg, Sonia Cohen, Katherine Prendergast, Sara Kryeziu, Richard L. White, Mitchell C. Posner, Nicholas D. Socci, Mrinal M. Gounder, Samuel Singer, Aimee M. Crago
Journal: Clinical Cancer Research (2023)

Abstract Purpose: This study sought to identify β-catenin targets that regulate desmoid oncogenesis and determine whether external signaling pathways, particularly those inhibited by sorafenib (e.g., PDGFRβ), affect these targets to alter natural history or treatment response in patients. Experimental Design: In vitro experiments utilized primary desmoid cell lines to examine regulation of β-catenin targets. Relevance of results was assessed in vivo using Alliance trial A091105 correlative biopsies. Results: CTNNB1 knockdown inhibited hypoxia-regulated gene expression in vitro and reduced levels of HIF1α protein. ChIP-seq identified ABL1 as a β-catenin transcriptional target that modulated HIF1α and desmoid cell proliferation. Abrogation of either CTNNB1 or HIF1A inhibited desmoid cell–induced VEGFR2 phosphorylation and tube formation in endothelial cell co-cultures. Sorafenib inhibited this activity directly but also reduced HIF1α protein expression and c-Abl activity while inhibiting PDGFRβ signaling in desmoid cells. Conversely, c-Abl activity and desmoid cell proliferation were positively regulated by PDGF-BB. Reduction in PDGFRβ and c-Abl phosphorylation was commonly observed in biopsy samples from patients after treatment with sorafenib; markers of PDGFRβ/c-Abl pathway activation in baseline samples were associated with tumor progression in patients on the placebo arm and response to sorafenib in patients receiving treatment. Conclusions: The β-catenin transcriptional target ABL1 is necessary for proliferation and maintenance of HIF1α in desmoid cells. Regulation of c-Abl activity by PDGF signaling and targeted therapies modulates desmoid cell proliferation, thereby suggesting a reason for variable biologic behavior between tumors, a mechanism for sorafenib activity in desmoids, and markers predictive of outcome in patients.
The CRTC-1 transcriptional domain is required for COMPASS complex-mediated longevity in C. elegans
Authors: Carlos G. Silva-García, Laura I. Láscarez-Lagunas, Katharina Papsdorf, Caroline Heintz, Aditi Prabhakar, Christopher S. Morrow, Lourdes Pajuelo Torres, Arpit Sharma, Jihe Liu, Monica P. Colaiácovo, Anne Brunet, William B. Mair
Journal: Nature Aging (2023)

Loss of function during aging is accompanied by transcriptional drift, altering gene expression and contributing to a variety of age-related diseases. CREB-regulated transcriptional coactivators (CRTCs) have emerged as key regulators of gene expression that might be targeted to promote longevity. Here we define the role of the Caenorhabditis elegans CRTC-1 in the epigenetic regulation of longevity. Endogenous CRTC-1 binds chromatin factors, including components of the COMPASS complex, which trimethylates lysine 4 on histone H3 (H3K4me3). CRISPR editing of endogenous CRTC-1 reveals that the CREB-binding domain in neurons is specifically required for H3K4me3-dependent longevity. However, this effect is independent of CREB but instead acts via the transcription factor AP-1. Strikingly, CRTC-1 also mediates global histone acetylation levels, and this acetylation is essential for H3K4me3-dependent longevity. Indeed, overexpression of an acetyltransferase enzyme is sufficient to promote longevity in wild-type worms. CRTCs, therefore, link energetics to longevity by critically fine-tuning histone acetylation and methylation to promote healthy aging.
Rise of synthetic yeast: Charting courses to new applications
Authors: Geoffrey J. Taghon, Elizabeth A. Strychalski
Journal: Cell Genomics (2023)

Microbes have long provided us with important capabilities, and the genome engineering of microbes has greatly empowered research and applications in biotechnology. This is especially true with the emergence of synthetic biology and recent advances in genome engineering to control microbial behavior. A fully synthetic, rationally designed genome promises opportunities for unprecedented control of cellular function. As a eukaryotic workhorse for research and industrial use, yeast is an organism at the forefront of synthetic biology; the tools and engineered cellular platform being delivered by the Sc2.0 consortium are enabling a new era of bespoke biology. This issue highlights recent advances delivered by this consortium, but hurdles remain to maximize the impact of engineered eukaryotic cells more broadly.
Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics
Authors: Benjamin A. Blount, Xinyu Lu, Maureen R.M. Driessen, Dejana Jovicevic, Mateo I. Sanchez, Klaudia Ciurkot, Yu Zhao, Stephanie Lauer, Robert M. McKiernan, Glen-Oliver F. Gowers, Fiachra Sweeney, Viola Fanfani, Evgenii Lobzaev, Kim Palacios-Flores, Roy S.K. Walker, Andy Hesketh, Jitong Cai, Stephen G. Oliver, Yizhi Cai, Giovanni Stracquadanio, Leslie A. Mitchell, Joel S. Bader, Jef D. Boeke, Tom Ellis
Journal: Cell Genomics (2023)

We describe construction of the synthetic yeast chromosome XI (synXI) and reveal the effects of redesign at non-coding DNA elements. The 660-kb synthetic yeast genome project (Sc2.0) chromosome was assembled from synthesized DNA fragments before CRISPR-based methods were used in a process of bug discovery, redesign, and chromosome repair, including precise compaction of 200 kb of repeat sequence. Repaired defects were related to poor centromere function and mitochondrial health and were associated with modifications to non-coding regions. As part of the Sc2.0 design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI, we show that these sites can facilitate induced extrachromosomal circular DNA (eccDNA) formation, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI contributes to our understanding of non-coding DNA elements, provides a useful tool for eccDNA study, and will inform future synthetic genome design.
Context-dependent neocentromere activity in synthetic yeast chromosome VIII
Authors: Stephanie Lauer, Jingchuan Luo, Luciana Lazar-Stefanita, Weimin Zhang, Laura H. McCulloch, Viola Fanfani, Evgenii Lobzaev, Max A.B. Haase, Nicole Easo, Yu Zhao, Fangzhou Yu, Jitong Cai, Joel S. Bader, Giovanni Stracquadanio, Jef D. Boeke, Lajari Anne, James S. Barger, Naz Belkaya, Kristin Boulier, Kirk Butler, Melanie Callaghan, Calvin Chang, Janice Chen, Xueni Jennifer Chen, In Young Cho, Elliot Choi, Woo Jin Choi, James Chuang, Ashley L. Cook, Eric Cooper, Nicholas Timothy Culbertson, Jessilyn Dunn, Charlotte Floria, Breeana Grogan Anderson, Nathalie P. Held, Emily Hsiao, Joseph-Kevin Igwe, Koeun Kang, Joana Karanxha, Marie Kelly, Arjun Khakhar, Chachrit Khunsriraksakul, John J. Kim, Dong Kim, Jin Wan Kim, Alex Lamb, David Sung Han Lee, Yoon Kyung Lee, Jongseuk Lim, Steffi Liu, Jeremy Lopez, Zhen A. Lu, Henry Ma, Jordan A. Mandel, Jessica Mao, Jordan Matelsky, Jonathan Merran, Rishikesh Mohan, Christopher Montoya, Sindurathy Murugan, Lisa Ni, Won Chan Oh, Youngrok Park, Laura Paulsen, Nick Phillips, Sudarshan Pinglay, Vikram Aditya Rajan, Garrett Ransom, Erin Rhoads, Praneeth Sanna, Emily Scher, Jinesh Shah, Ashwyn Sharma, Maya C. Shepardson, Joanne Song, Sainikhil Sontha, Venkatesh Srinivas, Scott Tan, Ang A. Tu, Skyler Uhl, Wang Xiaoyue, Fangzhou Yu, Justine Yu, Amadeus Zhu
Journal: Cell Genomics (2023)

Pioneering advances in genome engineering, and specifically in genome writing, have revolutionized the field of synthetic biology, propelling us toward the creation of synthetic genomes. The Sc2.0 project aims to build the first fully synthetic eukaryotic organism by assembling the genome of Saccharomyces cerevisiae. With the completion of synthetic chromosome VIII (synVIII) described here, this goal is within reach. In addition to writing the yeast genome, we sought to manipulate an essential functional element: the point centromere. By relocating the native centromere sequence to various positions along chromosome VIII, we discovered that the minimal 118-bp CEN8 sequence is insufficient for conferring chromosomal stability at ectopic locations. Expanding the transplanted sequence to include a small segment (∼500 bp) of the CDEIII-proximal pericentromere improved chromosome stability, demonstrating that minimal centromeres display context-dependent functionality.